Here's how it seems to be working for me. I have CAI and ARH long tube headers, and a custom tune to optimize the new breathing.

I recently started having engine misfires (long, and silly story around a simple loose plug wire not properly reconnected after header install!). Dealer knew full well what I'd done to the car. Took it in for the misfiring issue. He knew it was a custom tune as well. When he called GM for help diagnosing my issues (again, dont ask!), GM wanted him to upload my config to GM for analysis. He did not, and furthermore didnt even give GM the VIN he was calling about, but instead referred the issue back to me for a decision.

I took the car back to Ted Jannetty's shop in (not really) nearby CT (he did the tune). Ted spent 3 minutes on the laptop to find the issue, and get the car running right.

Get a device to load and save tunes, read and reset codes etc (Jannetty has a device for $300-ish from SCT for just this). GET the original tune saved before anything is done to re-tune (OH YEAH: Get a dyno run done BEFORE adding all the new goodies so you have a solid before-and-after baseline to reference). Once retuned, SAVE the new tune as well. In this fashion, if the dealer indeed flashes the car back to original, it's a simple matter of you restoring the custom tune.

But outright voiding warranty? No. As it was explained to me by the dealer, if an issue with the car is traced back to something done non-standard (i.e. not by the dealer), then they could simply deny repairs at no cost to you (e.g.: I add a supercharger and somehow blow out an engine component, or mayube smoke the clutch due to too much power, then the fix is on me).

Roughly speaking, and I mean BALLPARK...how much HP gain do headers provide? Does the GMPP air cleaner? The Catback exhaust?
I'm not gonna spend 2 grand for 25 hp gain, but 65 hp...that's a diff story.